mirror of
https://github.com/NixOS/nixpkgs.git
synced 2026-09-28 10:50:15 +00:00
142 lines
3.8 KiB
Nix
142 lines
3.8 KiB
Nix
{
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lib,
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stdenv,
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buildPackages,
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fetchurl,
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zlib,
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bzip2,
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perl,
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cpio,
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gawk,
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coreutils,
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curl,
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sqlite,
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llvmPackages,
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}:
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stdenv.mkDerivation (finalAttrs: {
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pname = "blast";
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version = "2.17.0";
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src = fetchurl {
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url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${finalAttrs.version}/ncbi-blast-${finalAttrs.version}+-src.tar.gz";
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sha256 = "sha256-UCBXqI6ZkONOYnWL4h6kdMwK1o1qY6LjeyNyrx5eoUc=";
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};
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sourceRoot = "ncbi-blast-${finalAttrs.version}+-src/c++";
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configureFlags = [
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# With flat Makefile we can use all_projects in order not to build extra.
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# These extra cause clang to hang on Darwin.
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"--with-flat-makefile"
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"--without-makefile-auto-update"
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"--with-dll" # build dynamic libraries (static are default)
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"--with-sqlite3=${sqlite.dev}"
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];
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makeFlags = [ "all_projects=app/" ];
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preConfigure = ''
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export NCBICXX_RECONF_POLICY=warn
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export PWD=$(pwd)
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export HOME=$PWD
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# The configure scripts wants to set AR="ar cr" unless it is already set in
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# the environment. Because stdenv sets AR="ar", the result is a bad call to
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# the assembler later in the process. Thus, we need to unset AR
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unset AR
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for awks in scripts/common/impl/is_log_interesting.awk \
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scripts/common/impl/report_duplicates.awk; do
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substituteInPlace $awks \
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--replace-fail "/usr/bin/awk" "${gawk}/bin/awk"
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done
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for mk in src/build-system/Makefile.meta.in \
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src/build-system/helpers/run_with_lock.c ; do
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substituteInPlace $mk \
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--replace-fail "/bin/rm" "${coreutils}/bin/rm"
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done
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for mk in src/build-system/Makefile.meta.gmake=no \
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src/build-system/Makefile.meta_l \
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src/build-system/Makefile.meta_r \
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src/build-system/Makefile.requirements \
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src/build-system/Makefile.rules_with_autodep.in; do
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substituteInPlace $mk \
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--replace-fail "/bin/echo" "${coreutils}/bin/echo"
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done
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for mk in src/build-system/Makefile.meta_p \
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src/build-system/Makefile.rules_with_autodep.in \
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src/build-system/Makefile.protobuf.in ; do
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substituteInPlace $mk \
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--replace-fail "/bin/mv" "${coreutils}/bin/mv"
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done
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substituteInPlace src/build-system/configure \
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--replace-fail "/bin/pwd" "${coreutils}/bin/pwd" \
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--replace-fail "/bin/ln" "${coreutils}/bin/ln"
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substituteInPlace src/build-system/configure.ac \
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--replace-fail "/bin/pwd" "${coreutils}/bin/pwd" \
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--replace-fail "/bin/ln" "${coreutils}/bin/ln"
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substituteInPlace src/build-system/Makefile.meta_l \
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--replace-fail "/bin/date" "${coreutils}/bin/date"
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'';
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depsBuildBuild = [ buildPackages.stdenv.cc ];
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nativeBuildInputs = [
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cpio
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perl
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];
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# perl is necessary in buildInputs so that installed perl scripts get patched
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# correctly
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buildInputs = [
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coreutils
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perl
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gawk
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zlib
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bzip2
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sqlite
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]
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++ lib.optionals stdenv.hostPlatform.isDarwin [
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llvmPackages.openmp
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];
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strictDeps = true;
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hardeningDisable = [ "format" ];
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postInstall = ''
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substituteInPlace $out/bin/get_species_taxids.sh \
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--replace-fail "/bin/rm" "${coreutils}/bin/rm"
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substituteInPlace $out/bin/update_blastdb.pl \
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--replace-fail 'qw(/usr/local/bin /usr/bin)' 'qw(${lib.getBin curl}/bin)'
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'';
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patches = [ ./no_slash_bin.patch ];
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enableParallelBuilding = true;
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# Many tests require either network access or locally available databases
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doCheck = false;
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meta = {
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description = "Basic Local Alignment Search Tool (BLAST) finds regions of similarity between biological sequences";
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homepage = "https://blast.ncbi.nlm.nih.gov/Blast.cgi";
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license = lib.licenses.publicDomain;
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platforms = lib.platforms.linux ++ [ "aarch64-darwin" ];
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maintainers = with lib.maintainers; [
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luispedro
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mulatta
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];
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};
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})
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